buildClassifier {cleanUpdTSeq}R Documentation

Build a Naive Bayes Classifier

Description

Computes the conditional a-posterior probabilities of a categorical class variable given independent predictor variables using the Bayes rule.

Usage

buildClassifier(
  Ndata.NaiveBayes,
  Pdata.NaiveBayes,
  upstream = 40L,
  downstream = 30L,
  wordSize = 6L,
  genome = Drerio,
  alphabet = c("ACGT")
)

Arguments

Ndata.NaiveBayes

A data.frame, containing features for the negative training data, described further in data.NaiveBayes.

Pdata.NaiveBayes

A data.frame, containing features for the positive training data, described further in data.NaiveBayes.

upstream

An integer(1) vector, length of upstream sequence to retrieve.

downstream

An integer(1) vector, length of downstream sequence to retrieve.

wordSize

An integer(1) vector, size of the kmer feature for the upstream sequence. wordSize = 6 should always be used.

genome

Name of the genome to get sequences from. To find out a list of available genomes, please type BSgenome::available.genomes() in R.

alphabet

A character(1) vector, a string containing DNA bases. By default, "ACTG".

Value

An object of class "naiveBayes".

Author(s)

Jianhong Ou

See Also

naiveBayes

Examples


if (interactive()){
    data(data.NaiveBayes)
    classifier <- buildClassifier(data.NaiveBayes$Negative, 
                                  data.NaiveBayes$Positive)
}


[Package cleanUpdTSeq version 1.31.0 Index]